Treatment and prognostic implications of strong PD-L1 expression in primary hepatic sarcomatoid carcinoma

Primary hepatic sarcomatoid carcinoma (HSC) is an extremely rare and aggressive subtype of primary liver cancer. HSC has uncertain pathogenesis and dismal prognosis with overall survival of only 8.3 months. The molecular alterations of HSC are also not well understood. In this study, the authors describe a patient who presented with a large liver mass. The patient underwent complete surgical resection and histological examination demonstrated HSC, infiltrating the stomach. PD-L1 was strongly positive in the tumor cells. The patient was started on anti-PD-L1 immunotherapy postsurgery and is doing well 15 months after surgical resection. Tumor whole exome sequencing revealed genetic alterations in TP53, NF2 and MAGEC3 genes, indicating their potential role in tumor development.

Understanding the Impact of Population and Cancer Type on Tumor Mutation Burden Scores: A Comprehensive Whole-Exome Study in Cancer Patients From India

PURPOSE

The purpose of this study was to understand the impact of population diversity and geographic variation on tumor mutation burden (TMB) scores across cancers and its implication on stratification of patients for immune checkpoint inhibitor (ICI) therapy.

MATERIALS AND METHODS

This retrospective study used whole-exome sequencing (WES) to profile 1,233 Indian patients with cancer across 30 different cancer types and to estimate their TMB scores. A WES-based pipeline was adopted, along with an indigenously developed strategy for arriving at true somatic mutations. A robust unsupervised machine learning approach was used to understand the distribution of TMB scores across different populations and within the population.

RESULTS

The results of the study showed a biphasic distribution of TMB scores in most cancers, with different threshold scores across cancer types. Patients with cancer in India had higher TMB scores compared with the Caucasian patients. We also observed that the TMB score value at 90th percentile (predicting high efficacy to ICI) was high in four different cancer types (sarcoma, ovary, head and neck, and breast) in the Indian cohort as compared with The Cancer Genome Atlas or public cohort. However, in lung and colorectal cancers, the TMB score distribution was similar between the two population cohorts.

CONCLUSION

The findings of this study indicate that it is crucial to benchmark both cancer-specific and population-specific TMB distributions to establish a TMB threshold for each cancer in various populations. Additional prospective studies on much larger population across different cancers are warranted to validate this observation to become the standard of care.

Biphenotypic Immunohistochemical Features and NTRK1 Amplification in Intermediate Cell Carcinoma of the Liver

Intermediate cell carcinoma is one of the rarest forms of primary liver cancer comprising relatively monomorphic populations of neoplastic epithelial cells demonstrating simultaneous positivity of both hepatocyte and cholangiocyte immunohistochemical markers. Here in, we describe an adult male patient who underwent left hepatectomy for a large liver tumor. The pathological and immunohistochemical analysis revealed the malignant primary liver cancer with intermediate cell morphology and mixed immunophenotypic features consistent with intermediate cell carcinoma. Furthermore, the genomic profiling using the Next-generation sequencing (NGS) platform demonstrated that there is a novel amplification with copy number gain 12 (12 gene copies) in the Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1) gene, being an oncogenic driver of intermediate cell carcinoma. This is the first case report with the amplification in NTRK1 and emphasizes the importance of molecular oncology.

Effect of Long-term Yoga Practice on Psychological outcomes in Breast Cancer Survivors

Aim:

Breast cancer has become a pandemic with an ever-increasing incidence. Although better diagnostics and treatment modalities have reduced mortality, a large number of survivors face cancer and treatment-related long-term symptoms. Many survivors are taking up yoga for improving the quality of life (QoL). The present study attempts to evaluate predictors of psychological states in breast cancer survivors with long-term yoga experience.

Materials and Methods:

A case–control study recruited early breast cancer survivors, 30–65 years, completing treatment > 6 months before recruitment, and grouped them based on prior yoga experience (BCY, n = 27) or naïve (BCN, n = 25). Demography, cancer history, diet, exercise habits, and yoga schedule were collected and tools to assess stress, anxiety, depression, general health, and QoL were administered. Multivariate linear regression was done to identify predictors of psychological variables.

Results:

BCY had significantly lower stress, anxiety, depression, better general health, and QoL (P < 0.001). Global QoL and trait anxiety were significantly predicted by Yoga practice; depression was predicted by yoga practice, annual income, and sleep quality; state anxiety was predicted by Yoga practice and income; and stress was predicted by Yoga practice and sleep quality.

Conclusion:

Results indicate that breast cancer survivors, doing yoga, have better psychological profiles and are able to deal with demanding situations better. The psycho-oncogenic model of cancer etiology suggests that a better psychological state in survival has the potential to improve prognosis and survival outcomes and Yoga may be a suitable practice for staying cancer-free for a longer time.

Prevalence of KRAS mutations in metastatic colorectal cancer: A retrospective observational study from India

BACKGROUND

One of the genetic alterations implicated in tumor progression in colorectal cancers (CRCs) are abnormalities in Kristen Rat Sarcoma (KRAS) gene. Evaluation of KRAS mutation status is an important prognostic factor and has predictive value in deciding first line therapy based on monoclonal antibodies such as Cetuximab and Panitumumab in metastatic CRCs.

MATERIALS AND METHODS

In this retrospective study, we analyzed 7 different somatic mutations in Exon 2 of KRAS gene in 299 unselected incidental CRC patients who visited the hospital for clinical management during the period 2009-2013. Most of the tumors were primarily originating from colon and rectum; nevertheless, there were a few from rectosigmoid, sigmoid, ceacum and anal canal in the study group. Genomic DNA extracted from paraffin embedded tumor tissues was screened for 7 point mutations located in Codons 12 and 13 of KRAS gene, using Scorpions amplified refractory mutation system real time polymerase chain reaction technology. Statistical analysis was performed to assess bivariate relationship between different variables that includes: mutation status, mutation type, tumor location, tumor morphology, age and sex.

RESULTS

Prevalence of mutation in Codons 12 and 13 was 42.8% in the study group. Well-differentiated tumors had significantly more mutation positivity than moderately and poorly differentiated tumors (P = 0.001). 92% of the mutations were from Codon 12 and 8% in Codon 13. Glycine to Arginine was relatively more common in rectosigmoid followed by ceacum, while Glycine to Alanine mutation was relatively more prevalent in sigmoid, followed by rectum and rectosigmoid.

CONCLUSION

The results suggest a prevalence of KRAS mutation at 42.8% in Indian population indicating that this testing is very crucial for targeted therapy management in metastatic CRC in India. Further analysis on mutation status of other homologues such as NRAS and downstream partner, v-raf murine sarcoma viral oncogene homolog B1, would add value to understanding the role of anti-epidermal growth factor receptor therapy in CRC management.

Genetics and Breast Cancer - Oncologists Perspectives

Breast cancer is the most common cancer in women worldwide. The clinical outcomes of which, have improved in the past decade, primarily due early diagnosis and multimodal management. Understanding of the disease biology with findings from omics-based research and molecular genetic characterization of the disease has been an important component of the therapy in the past 10 years. There is a need to understand the variations in individuals at the molecular level to enable in sub-classification of the different disease phenotypes and if possible to tailor the treatment to the patient. This article attempts to review the beneficial role of genetics in various facets of breast cancer management, in modern scientific medicine.

ATP forms a stable complex with the essential histidine kinase WalK (YycG) domain

In Bacillus subtilis, the WalRK (YycFG) two-component system coordinates murein synthesis with cell division. It regulates the expression of autolysins that function in cell-wall remodeling and of proteins that modulate autolysin activity. The transcription factor WalR is activated upon phosphorylation by the histidine kinase WalK, a multi-domain homodimer. It autophosphorylates one of its histidine residues by transferring the γ-phosphate from ATP bound to its ATP-binding domain. Here, the high-resolution crystal structure of the ATP-binding domain of WalK in complex with ATP is presented at 1.61 Å resolution. The bound ATP remains intact in the crystal lattice. It appears that the strong binding interactions and the nature of the binding pocket contribute to its stability. The triphosphate moiety of ATP wraps around an Mg(2+) ion, providing three O atoms for coordination in a near-ideal octahedral geometry. The ATP molecule also makes strong interactions with the protein. In addition, there is a short contact between the exocyclic O3' of the sugar ring and O2B of the β-phosphate, implying an internal hydrogen bond. The stability of the WalK-ATP complex in the crystal lattice suggests that such a complex may exist in vivo poised for initiation of signal transmission. This feature may therefore be part of the sensing mechanism by which the WalRK two-component system is so rapidly activated when cells encounter conditions conducive for growth.

Crystal structure of the transcriptional repressor PagR of Bacillus anthracis

PagR is a transcriptional repressor in Bacillus anthracis that controls the chromosomal S-layer genes eag and sap, and downregulates the protective antigen pagA gene by direct binding to their promoter regions. The PagR protein sequence is similar to those of members of the ArsR repressor family involved in the repression of arsenate-resistance genes in numerous bacteria. The crystal structure of PagR was solved using multi-wavelength anomalous diffraction (MAD) techniques and was refined with 1.8 A resolution diffraction data. The PagR molecules form dimers, as observed in all SmtB/ArsR repressor family proteins. In the crystal lattice four PagR dimers pack together to form an inactive octamer. Model-building studies suggest that the dimer binds to a DNA duplex with a bend of around 4 degrees.

Sporulation Phosphorelay Proteins and Their Complexes: Crystallographic Characterization

Bacteria use two-component systems to adapt to changes in environmental conditions. In response to deteriorating conditions of growth, certain types of bacteria form spores instead of proceeding with cell division. The formation of spores is controlled by an expanded version of two-component systems called the phosphorelay. The phosphorelay comprises a primary kinase that receives the signal/stimulus and undergoes autophosphorylation, followed by two intermediate messengers that regulate the flow of the phosphoryl group to the ultimate response regulator/transcription factor. Sporulation is initiated when the level of phosphorylation of the transcription factor reaches a critical point. This chapter describes efforts to understand the mechanism of initiation of sporulation at the molecular level using X-ray crystallography as a tool. Structural analyses of individual members, as well as their complexes, provide insight into the mechanism of phosphoryl transfer and the origin of specificity in signal transduction.